T0404

Targets
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T0404

PII-like signaling protein (YP_323533.1) from Anabaena variabilis

Target type: Server only

Target sequence:

>T0404 YP_323533.1, Anabaena variabilis, 110 residues
MSKRANKLVIVTEKVLLKKVAKIIEEAGATGYTVVDTGGKGSRNVRSTGKPNTSDTDSNVKFEVLTENREMAEKIADQVAIKFFTDYAGIIYICEAEVLYGRTFCGPDGC

Structure:
Method: X-ray, res=2.35Å, R/Rfree=0.23/0.27
Determined by: JCSG
PDB ID: 3dfe

3dfe_A cartoon
Cartoon diagram of 404: 3dfe chain A

PyMOL of 3dfe

Domains:  PyMOL of domains

Single domain protein.

Structure classification:

Ferredoxin-like fold.

CASP category:

Comparative modeling:easy.

Closest templates:

2cz4.

Target sequence - PDB file inconsistencies:

T0404    3dfe.pdb    T0404.pdb    PyMOL    PyMOL of domains    

T0404    1 MSKRANKLVIVTEKVLLKKVAKIIEEAGATGYTVVDTGGKGSRNVRSTGKPNTSDTDSNVKFEVLTENREMAEKIADQVAIKFFTDYAGIIYICEAEVLYGRTFCGPDGC 110
           ~||||||||||||||||||||||||||||||||||||||~~~~~~~~~~~~~~~~~~||||||||||||||||||||||||||||||||||||||||||||~~~~~~~~~
3dfeA    2 -SKRANKLVIVTEKVLLKKVAKIIEEAGATGYTVVDTGG------------------SNVKFEVLTENREMAEKIADQVAIKFFTDYAGIIYICEAEVLYG--------- 101

Residue change log: change 71, MSE to MET;

Single domain protein: target 2-39, 58-101 ; pdb 2-39, 58-101

Sequence classification:

GlnB-like superfamily in SCOP.

Server predictions:

T0404:pdb 2-101:seq 2-101:CM_easy;   alignment

distribution of first scores
First models for T0404: Gaussian kernel density estimation for GDT-TS scores of the first server models, plotted at various bandwidths (=standard deviations). The GDT-TS scores are shown as a spectrum along the horizontal axis: each bar represents first server model. The bars are colored green, gray and black for top 10, bottom 25% and the rest of servers. The family of curves with varying bandwidth is shown. Bandwidth varies from 0.3 to 8.2 GDT-TS % units with a step of 0.1, which corresponds to the color ramp from magenta through blue to cyan. Thicker curves: red, yellow-framed brown and black, correspond to bandwidths 1, 2 and 4 respectively.

click on a score in the table below to display the model in PyMOL

# GROUP ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ ↓ GROUP #
T0404 T0404 T0404 T0404
First score First Z-score Best score Best Z-score
1 MULTICOM−REFINE 92.68 89.63 92.08 1.21 1.52 1.13 92.68 89.74 92.41 1.10 1.45 1.01 MULTICOM−REFINE 1
2 MUProt 92.38 89.33 92.07 1.17 1.48 1.12 92.68 90.65 92.40 1.10 1.60 1.01 MUProt 2
3 RAPTOR 91.77 85.67 92.65 1.08 0.99 1.20 91.77 85.67 92.65 0.93 0.78 1.05 RAPTOR 3
4 fais−server 91.77 84.25 90.12 1.08 0.80 0.88 91.77 84.25 90.12 0.93 0.54 0.69 fais−server 4
5 Pcons_dot_net 91.77 81.00 91.56 1.08 0.37 1.06 92.38 84.25 92.23 1.04 0.54 0.99 Pcons_dot_net 5
6 Pcons_multi 91.77 81.00 91.56 1.08 0.37 1.06 91.77 81.00 91.74 0.93 0.00 0.92 Pcons_multi 6
7 MUSTER 91.46 86.38 91.77 1.03 1.08 1.09 91.77 86.38 92.05 0.93 0.89 0.96 MUSTER 7
8 BAKER−ROBETTA 91.46 85.37 91.94 1.03 0.95 1.11 91.46 85.37 91.94 0.87 0.73 0.95 BAKER−ROBETTA 8
9 3Dpro 91.46 77.44 91.61 1.03 -0.11 1.07 91.46 82.22 91.61 0.87 0.21 0.90 3Dpro 9
10 keasar−server 91.16 84.25 90.96 0.98 0.80 0.99 91.16 84.25 90.96 0.82 0.54 0.81 keasar−server 10
11 PS2−server 90.85 86.38 90.14 0.94 1.08 0.88 90.85 86.38 90.14 0.76 0.89 0.70 PS2−server 11
12 Zhang−Server 90.85 85.98 90.65 0.94 1.03 0.95 91.77 90.24 91.79 0.93 1.53 0.93 Zhang−Server 12
13 FEIG 90.85 83.74 91.14 0.94 0.73 1.01 90.85 86.38 91.14 0.76 0.89 0.84 FEIG 13
14 HHpred4 90.55 87.09 91.64 0.89 1.18 1.07 90.55 87.09 91.64 0.71 1.01 0.91 HHpred4 14
15 HHpred5 90.55 87.09 91.64 0.89 1.18 1.07 90.55 87.09 91.64 0.71 1.01 0.91 HHpred5 15
16 YASARA 90.55 79.98 89.04 0.89 0.23 0.75 90.55 80.79 89.26 0.71 -0.03 0.57 YASARA 16
17 PSI 90.55 78.15 91.81 0.89 -0.01 1.09 90.55 78.15 91.81 0.71 -0.47 0.93 PSI 17
18 circle 90.24 86.79 89.47 0.85 1.14 0.80 91.46 87.81 92.09 0.87 1.13 0.97 circle 18
19 FFASsuboptimal 90.24 83.74 89.01 0.85 0.73 0.74 91.16 84.86 91.01 0.82 0.64 0.82 FFASsuboptimal 19
20 FUGUE_KM 90.24 83.33 89.23 0.85 0.68 0.77 90.24 83.33 89.23 0.65 0.39 0.57 FUGUE_KM 20
21 pipe_int 89.94 87.30 88.96 0.80 1.21 0.74 89.94 87.30 88.96 0.60 1.05 0.53 pipe_int 21
22 HHpred2 89.94 86.28 91.70 0.80 1.07 1.08 89.94 86.28 91.70 0.60 0.88 0.91 HHpred2 22
23 FFASflextemplate 89.94 85.06 88.29 0.80 0.91 0.66 90.55 85.06 89.41 0.71 0.68 0.60 FFASflextemplate 23
24 FAMSD 89.94 81.40 89.33 0.80 0.42 0.78 90.85 87.19 89.50 0.76 1.03 0.61 FAMSD 24
25 BioSerf 89.63 81.50 86.67 0.75 0.43 0.45 89.63 81.50 86.67 0.54 0.09 0.21 BioSerf 25
26 MULTICOM−CLUSTER 89.63 76.73 90.35 0.75 -0.20 0.91 90.85 85.77 90.41 0.76 0.79 0.73 MULTICOM−CLUSTER 26
27 huber−torda−server 89.33 86.89 87.52 0.71 1.15 0.56 89.33 86.89 87.52 0.49 0.98 0.33 huber−torda−server 27
28 Poing 89.33 82.83 89.40 0.71 0.61 0.79 89.33 82.83 89.40 0.49 0.31 0.59 Poing 28
29 FFASstandard 89.02 83.74 88.83 0.66 0.73 0.72 90.24 83.74 89.01 0.65 0.46 0.54 FFASstandard 29
30 Phyre2 89.02 81.71 89.18 0.66 0.46 0.77 89.02 81.71 89.18 0.43 0.12 0.56 Phyre2 30
31 Phragment 89.02 81.71 89.18 0.66 0.46 0.77 89.02 81.71 89.18 0.43 0.12 0.56 Phragment 31
32 pro−sp3−TASSER 87.50 81.20 88.26 0.44 0.39 0.65 89.33 84.65 90.37 0.49 0.61 0.73 pro−sp3−TASSER 32
33 3DShot2 87.19 82.72 84.80 0.39 0.60 0.22 87.19 82.72 84.80 0.10 0.29 -0.05 3DShot2 33
34 MULTICOM−CMFR 86.58 80.49 82.42 0.30 0.30 -0.07 92.07 88.82 91.62 0.99 1.30 0.90 MULTICOM−CMFR 34
35 LEE−SERVER 86.28 81.81 88.05 0.25 0.48 0.63 88.42 83.54 89.69 0.32 0.42 0.63 LEE−SERVER 35
36 mGenTHREADER 86.28 78.15 82.97 0.25 -0.01 -0.00 86.28 78.15 82.97 -0.06 -0.47 -0.30 mGenTHREADER 36
37 Pushchino 85.67 84.45 77.91 0.16 0.83 -0.63 85.67 84.45 77.91 -0.18 0.58 -1.01 Pushchino 37
38 METATASSER 85.37 82.11 86.24 0.12 0.52 0.40 89.63 85.16 88.29 0.54 0.69 0.44 METATASSER 38
39 Fiser−M4T 84.76 82.11 75.77 0.02 0.52 -0.90 84.76 82.11 75.77 -0.34 0.19 -1.31 Fiser−M4T 39
40 Frankenstein 81.40 78.15 79.62 -0.48 -0.01 -0.42 82.32 78.15 82.12 -0.78 -0.47 -0.42 Frankenstein 40
41 Phyre_de_novo 80.79 76.73 76.51 -0.57 -0.20 -0.80 89.02 82.11 89.20 0.43 0.19 0.57 Phyre_de_novo 41
42 FALCON 80.79 70.22 78.60 -0.57 -1.07 -0.55 91.77 83.64 92.26 0.93 0.44 0.99 FALCON 42
43 SAM−T02−server 80.49 77.85 63.75 -0.62 -0.05 -2.39 80.49 77.85 63.75 -1.12 -0.52 -2.98 SAM−T02−server 43
44 GeneSilicoMetaServer 80.18 73.88 76.97 -0.66 -0.58 -0.75 90.85 79.57 90.91 0.76 -0.23 0.80 GeneSilicoMetaServer 44
45 panther_server 80.18 72.05 79.06 -0.66 -0.82 -0.49 82.01 78.96 79.07 -0.84 -0.33 -0.85 panther_server 45
46 3D−JIGSAW_AEP 79.27 75.20 76.92 -0.80 -0.40 -0.75 79.27 75.20 77.42 -1.34 -0.96 -1.08 3D−JIGSAW_AEP 46
47 GS−KudlatyPred 79.27 73.78 78.32 -0.80 -0.59 -0.58 79.27 73.78 78.32 -1.34 -1.19 -0.95 GS−KudlatyPred 47
48 3D−JIGSAW_V3 78.96 72.46 77.99 -0.84 -0.77 -0.62 78.96 72.87 78.00 -1.39 -1.34 -0.99 3D−JIGSAW_V3 48
49 MULTICOM−RANK 78.66 75.61 78.25 -0.89 -0.35 -0.59 79.88 75.61 78.25 -1.23 -0.89 -0.96 MULTICOM−RANK 49
50 CpHModels 78.66 74.59 72.53 -0.89 -0.49 -1.30 78.66 74.59 72.53 -1.45 -1.06 -1.76 CpHModels 50
51 forecast 78.35 74.29 77.43 -0.94 -0.53 -0.69 82.62 79.57 79.16 -0.73 -0.23 -0.83 forecast 51
52 Distill 78.05 74.19 76.12 -0.98 -0.54 -0.85 79.57 77.54 76.38 -1.28 -0.57 -1.22 Distill 52
53 OLGAFS 77.74 74.08 72.73 -1.03 -0.55 -1.27 84.76 83.54 77.06 -0.34 0.42 -1.13 OLGAFS 53
54 nFOLD3 76.22 70.73 72.97 -1.26 -1.00 -1.24 82.62 75.71 79.80 -0.73 -0.87 -0.74 nFOLD3 54
55 SAM−T08−server 75.92 68.60 74.74 -1.30 -1.28 -1.02 80.49 76.42 74.74 -1.12 -0.75 -1.45 SAM−T08−server 55
56 COMA 75.31 64.13 73.47 -1.39 -1.88 -1.18 76.22 64.13 74.34 -1.89 -2.79 -1.50 COMA 56
57 GS−MetaServer2 75.00 57.83 69.59 -1.44 -2.72 -1.66 75.00 59.45 69.97 -2.11 -3.56 -2.11 GS−MetaServer2 57
58 Pcons_local 74.69 70.22 71.33 -1.48 -1.07 -1.45 76.52 72.26 77.40 -1.84 -1.44 -1.08 Pcons_local 58
59 COMA−M 74.69 67.38 73.85 -1.48 -1.45 -1.13 75.00 67.38 73.87 -2.11 -2.25 -1.57 COMA−M 59
60 SAM−T06−server 73.78 70.73 74.32 -1.62 -1.00 -1.08 81.10 76.42 77.59 -1.00 -0.75 -1.05 SAM−T06−server 60
61 mariner1 72.87 64.53 75.60 -1.76 -1.83 -0.92 79.57 73.17 79.24 -1.28 -1.29 -0.82 mariner1 61
62 rehtnap 72.56 63.62 69.05 -1.80 -1.95 -1.73 74.69 63.62 70.26 -2.17 -2.87 -2.07 rehtnap 62
63 ACOMPMOD 70.73 65.24 67.89 -2.08 -1.73 -1.87 70.73 65.24 67.89 -2.89 -2.60 -2.40 ACOMPMOD 63
64 MUFOLD−Server 70.12 57.93 67.91 -2.17 -2.70 -1.87 72.26 64.74 68.34 -2.61 -2.69 -2.34 MUFOLD−Server 64
65 LOOPP_Server 64.94 57.22 63.98 -2.95 -2.80 -2.36 78.96 74.49 77.64 -1.39 -1.07 -1.04 LOOPP_Server 65
66 FOLDpro 60.37 46.24 63.76 -3.63 -4.26 -2.38 63.41 56.30 65.22 -4.21 -4.08 -2.77 FOLDpro 66
67 FALCON_CONSENSUS 51.83 42.07 45.34 -4.91 -4.82 -4.67 91.77 83.64 92.26 0.93 0.44 0.99 FALCON_CONSENSUS 67
68 RBO−Proteus 46.95 34.35 47.67 -5.64 -5.84 -4.38 46.95 34.35 47.67 -7.20 -7.72 -5.22 RBO−Proteus 68
69 MUFOLD−MD 33.54 31.00 41.33 -7.65 -6.29 -5.16 51.83 42.07 47.38 -6.31 -6.44 -5.26 MUFOLD−MD 69
70 RANDOM 21.74 18.69 21.74 -9.42 -7.93 -7.59 21.74 18.69 21.74 -11.77 -10.31 -8.83 RANDOM 70
71 schenk−torda−server 21.04 17.18 26.28 -9.53 -8.13 -7.03 26.22 21.14 31.00 -10.96 -9.90 -7.54 schenk−torda−server 71
72 mahmood−torda−server 19.82 17.79 23.85 -9.71 -8.05 -7.33 21.65 18.39 25.05 -11.79 -10.36 -8.37 mahmood−torda−server 72
73 BHAGEERATH                   -9.42 -7.93 -7.59                   -11.77 -10.31 -8.83 BHAGEERATH 73
74 test_http_server_01                   -9.42 -7.93 -7.59                   -11.77 -10.31 -8.83 test_http_server_01 74